| Package | Description |
|---|---|
| net.maizegenetics.analysis |
Plugins and tools for analysis genetics and genomics.
|
| net.maizegenetics.analysis.association |
Approaches for conducting GWAS including GLM and MLM approaches
|
| net.maizegenetics.analysis.avro | |
| net.maizegenetics.analysis.b4r | |
| net.maizegenetics.analysis.chart |
Charts used to plot data including scatter, QQ, and Manhattan plots
|
| net.maizegenetics.analysis.clustering |
The clustering package provides classes to cluster genotype sequence for the purpose of identifying common haplotypes.
|
| net.maizegenetics.analysis.data |
Plugins for manipulating datasets including reading, writing, and combining datasets
|
| net.maizegenetics.analysis.distance |
Methods for estimating the genetic distance between taxa
|
| net.maizegenetics.analysis.filter |
Plugins for filtering GenotypeTables by site or taxa
|
| net.maizegenetics.analysis.gbs |
The GBS package provide plugins and analysis approaches for genotyping by sequencing.
|
| net.maizegenetics.analysis.gbs.neobio | |
| net.maizegenetics.analysis.gbs.pana |
The Pan-genome Atlas (PanA) package provides plugins for genetic mapping high density sequence tags, which can be used for GBS and WGS data
|
| net.maizegenetics.analysis.gbs.repgen | |
| net.maizegenetics.analysis.gbs.v2 | |
| net.maizegenetics.analysis.gobii | |
| net.maizegenetics.analysis.imputation |
Methods for genotypic imputation including Viterbi HMM, FSFHap, and FILLIN
|
| net.maizegenetics.analysis.modelfitter |
The modelfitter package contains classes that use various methods to fit multiple variant
sites to a GWAS model.
|
| net.maizegenetics.analysis.monetdb | |
| net.maizegenetics.analysis.numericaltransform |
Methods for transformation of numerical datasets including principle components analysis, KNN imputation, etc.
|
| net.maizegenetics.analysis.phg | |
| net.maizegenetics.analysis.popgen |
Analysis methods for estimating linkage disequilibrium and sequence diversity
|
| net.maizegenetics.analysis.rna | |
| net.maizegenetics.analysis.tree |
Plugins for creating trees based on genetic distance and displaying trees
|
| net.maizegenetics.analysis.workflow | |
| net.maizegenetics.dna |
Data structures involved in genetics, genomes, and the representation of DNA variation.
|
| net.maizegenetics.dna.map |
Supports genetic and physical map representations of genomes including their annotation.
|
| net.maizegenetics.dna.pd |
Supports annotations or polymorphisms descriptors (pds) of a genome.
|
| net.maizegenetics.dna.read |
Data structures for holding raw sequence data (only Fastq currently), including Illumina, PacBio, Nanapore, etc.
|
| net.maizegenetics.dna.snp |
Data structures for holding SNP and indel variation across taxa (samples) and genomic positions.
|
| net.maizegenetics.dna.snp.bit |
Support for bit level encoding of allele presence and absence.
|
| net.maizegenetics.dna.snp.byte2d | |
| net.maizegenetics.dna.snp.genotypecall |
Genotype calls for all the taxa and genomic positions scored.
|
| net.maizegenetics.dna.snp.io |
Support for reading and writing GenotypeTables to various file formats.
|
| net.maizegenetics.dna.snp.score |
Support for site scores (for example quality scores or imputation accuracy).
|
| net.maizegenetics.dna.tag |
Data structures for holding tags (contiguous DNA).
|
| net.maizegenetics.gui |
Classes for the graphical display of GenotypeTables and other graphical elements
|
| net.maizegenetics.matrixalgebra.decomposition |
Matrix decomposition methods used by GWAS and GS analysis tools
|
| net.maizegenetics.matrixalgebra.Matrix |
Matrix algebra package that makes connections to various library optimization including parallelized and native code.
|
| net.maizegenetics.phenotype |
Phenotype (future) and Trait (deprecated) currently both define classes for holding trait data.
|
| net.maizegenetics.pipeline |
Runs TASSEL Pipeline (Command Line Interface) built with a set of plugins.
|
| net.maizegenetics.plugindef |
Plugin interface used to make analysis code compatible with TASSEL GUI or TASSEL pipeline.
|
| net.maizegenetics.prefs |
Preferences used by TASSEL.
|
| net.maizegenetics.progress |
Components used to track and display plugin progress.
|
| net.maizegenetics.stats.EMMA |
Class for implementation of the EMMA algorithm often used in GWAS.
|
| net.maizegenetics.stats.linearmodels |
Range of statistical and higher level linear algebra functions
|
| net.maizegenetics.stats.math |
Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials,
random numbers, special function etc.
|
| net.maizegenetics.stats.PCA |
Classes and methods for principle components analysis
|
| net.maizegenetics.stats.statistics |
Classes with useful for statistics (normal distribution,
Gamma distribution, chi-square distribution, exponential distribution,
likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)
|
| net.maizegenetics.tassel |
TASSEL graphical user interface classes and images
|
| net.maizegenetics.taxa |
Taxa package supports lists of taxa (samples) and their annotation.
|
| net.maizegenetics.taxa.distance |
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
|
| net.maizegenetics.taxa.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
| net.maizegenetics.util |
Provide basic utilities classes and methods used the entire code base.
|
| net.maizegenetics.util.db |
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